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The beginnings of Proteus AG can be traced to the founding in 2005 of the Prometheus Foundation, a philanthropic organization dedicated to the exploration of space and undersea. The Prometheus Foundation was founded by an industrialist and biotechnologist named Frederick Goldammer, and it was known for its financial aid in the wake of several national German catastrophes such as the Cattenom meltdown in 2008 and the floods of 2011.

Goldammer became involved in the North-Sea Arcology Project in 2030. The aim of the North-Sea Arcology Project was simply to create habitats in the North Sea, reclaiming land lost to flooding. This put Goldammer in contact with Gideon Schreiber, an alter ego of the Great Dragon Nachtmeister. Official construction on the Arcology Project did not begin until 2038.

Frederick Goldammer's death in 2037 moved control of the Prometheus Foundation to his granddaughter, Yasmin Goldammer-Sorensen. With her grandfather's wealth and the Foundation's resources, together with a firm called Van Ronzelen Umwelttechnick-GmbH founded by Nachtmeister, Yasmin and several other supporters (known as the Founders or the Fathers) incorporated the Prometheus Foundation in 2040 as "Proteus". It wasn't until January 1, 2049, that the corporation Proteus AG was officially created, headquartered on the German island of Helgoland.

Proteus AG was involved in a few minor events during the early years of the 2050s. Proteus was recognized as a AA-megacorporation by the corporate court on July 6, 2051, and it was given extraterritoriality status. Proteus AG contributed to the coalition of troops the reclaimed Berlin in August 2055. In March 2057, Proteus was given permission by the French government to use the Devil Islands as a space launch pad, in return for the favor of sending French satellites into space.

Proteus AG's acumen lay in playing off larger AAA-corporations (specifically Cross Applied Technologies, Shiawase, and Yamatetsu) as well as smaller German corporations such as Ruhrmetall, AGC, and IFMU, in a sort of "Research middle man" position. Through these alliances, Proteus was able to leech off of the profitable research from other corporations while also profiting off the brokerage of the same research information to those corporations.

In June and July of 2063, Proteus engaged in a sea conflict with Ares, with both sides sinking submarines in the process. This ended with an Ares retaliatory orbital strike against the Rømø arkoblock in July of 2063 via Thor shot. This was resolved by the Corporate Court in August of 2063. Instead of an Omega Order, the rule of Proteus was handed back over to the Prometheus Foundation under the helm of Kevin Goldammer, along with a new board of directors appointed to the Foundation. The new Board of Directors became responsible for paying reparations to the other corporations that Proteus was leeching from, as well as pointing Proteus into new directions through its successful arkoblock and space ventures.